Input data and parameters 

Input

Analysis date: Tue Oct 31 09:45:11 GMT 2023
BAM file: SRX7354342.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 39,258,126 / 39,223,657
Number of aligned pairs (without duplicates): 39,217,100
Total number of alignments: 82,720,236
Number of secondary alignments: 4,238,453
Number of non-unique alignments: 7,101,497
Aligned to genes: 65,369,703
Ambiguous alignments: 216,867
No feature assigned: 9,789,173
Missing chromosome in annotation: 242,996
Not aligned: 9,131,441

Reads genomic origin

Exonic: 65,369,703 / 86.98%
Intronic: 6,894,317 / 9.17%
Intergenic: 2,894,856 / 3.85%
Intronic/intergenic overlapping exon: 2,613,774 / 3.48%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.15
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 22,810,658
ACCT 5.32%
AGGT 4.58%
AGGA 3.6%
ATCT 3.58%
TCCT 3.33%
GCCT 3.19%
AGCT 2.85%
AGGC 2.37%
AGAT 2.37%
CCCT 2.14%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis